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Maximum-Likelihood Multi-Reference Refinement for Electron Microscopy Images
- J. Molecular Biology
, 2005
"... A maximum-likelihood approach to multi-reference image refinement is presented. In contrast to conventional cross-correlation refinement, the new approach includes a formal description of the noise, implying that it is especially suited to cases with low signal-to-noise ratios. Application of this a ..."
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Cited by 17 (3 self)
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A maximum-likelihood approach to multi-reference image refinement is presented. In contrast to conventional cross-correlation refinement, the new approach includes a formal description of the noise, implying that it is especially suited to cases with low signal-to-noise ratios. Application of this approach to a cryo-electron microscopy dataset revealed two major classes for projections of simian virus 40 large T-antigen in complex with an asymmetric DNA-probe, containing the origin of simian virus 40 replication. Strongly bent projections of dodecamers showed density that may be attributed to the complexed double-stranded DNA, while almost straight projections revealed a twist in the relative orientation of the hexameric subunits. This new level of detail for large T-antigen projections was not detected using conventional techniques. For a negative stain dataset, maximum-likelihood refinement yielded results that were practically identical to those obtained using conventional multi-reference refinement. Results obtained using simulated data suggest that the efficiency of the maximum-likelihood approach may be further enhanced by explicitly incorporating the microscope contrast transfer function in the image formation model.
Weighted distance transforms generalized to modules and their computation on point lattices
, 2008
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Single-particle 3D reconstruction from cryo-electron microscopy images on GPU
- in: Proceedings of the International conference on Supercomputing ICS
, 2009
"... Single-particle 3D reconstruction from cryo-electron microscopy (cryo-EM) images is a kernel application of biological molecules analysis, as the computational requirement of which is now beyond PetaFlop for a high-resolution 3D structure. In this paper, we quantitatively analyze the workload, com-p ..."
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Single-particle 3D reconstruction from cryo-electron microscopy (cryo-EM) images is a kernel application of biological molecules analysis, as the computational requirement of which is now beyond PetaFlop for a high-resolution 3D structure. In this paper, we quantitatively analyze the workload, com-putational intensity and memory performance of the ap-plication, parallelize it on an emerging multicore architec-ture GPU-CUDA. Further we apply a percolation technique to decouple computation with memory operations and or-chestrate thread-data mapping to reduce the overhead off-chip memory operations. Finally we tested our optimiza-tion strategy on a popular open-source package EMAN to GPU-CUDA, which achieves a relative speedup of about 10X to the original CPU-only EMAN. The experimental results also show that the proposed percolation program-ming greatly improves utilization of memory bandwidth and floating-point units.
Molecular architecture of a multifunctional MCM complex
, 2011
"... DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a p ..."
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DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a primase domain constituting an integrative arrangement of two essential activities for replication. We have isolated this helicase–primase complex (BcMCM) showing that it can bind DNA and displays not only helicase and primase but also DNA polymerase activity. Using single-particle electron microscopy and 3D reconstruction, we obtained structures of BcMCM using ATPcS or ADP in the absence and presence of DNA. The complex depicts the typical hexameric ring shape. The dissection of the unwinding mechanism using site-directed mutagenesis in the Walker A, Walker B, arginine finger and the helicase channels, suggests that the BcMCM complex unwinds DNA following the extrusion model similarly to the E1 helicase from papillomavirus.
Grid Computing in 3D-EM Image Processing using Xmipp
"... * These authors contributed equally to this work Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amounts of data, and voluminous computing requirements. Here, we report our first experience with grid computing in this area. We present an interface between ..."
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* These authors contributed equally to this work Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amounts of data, and voluminous computing requirements. Here, we report our first experience with grid computing in this area. We present an interface between grid computing middleware and our image processing package Xmipp. The efficacy of this approach was illustrated with an Xmipp application for estimation of the contrast transfer function. In addition, we report our experience with grid computing in the development of a novel image refinement algorithm based on maximum likelihood principles. Its extensive CPUrequirements might have seriously hampered the algorithm development, if not for the farreaching resources of grid computing. Our results suggest that electron microscopy image processing may be particularly well suited for grid computing. 1.
Cryoelectron Microscopy of Icosahedral Virus Particles
"... With the rapid progresses in both instrumentation and computing, it is increasingly straightforward and routine to determine the structures of icosahedral viruses to subnano-meter resolutions (6–10 Å) by cryoelectron microscopy and image reconstruction. In this resolution range, secondary structure ..."
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With the rapid progresses in both instrumentation and computing, it is increasingly straightforward and routine to determine the structures of icosahedral viruses to subnano-meter resolutions (6–10 Å) by cryoelectron microscopy and image reconstruction. In this resolution range, secondary structure elements of protein subunits can be clearly dis-cerned. Combining the three-dimensional density map and bioinformatics of the protein components, the folds of the virus capsid shell proteins can be derived. This chapter will describe the experimental and computational procedures that lead to subnanometer resolu-tion structural determinations of icosahedral virus particles. In addition, we will describe how to extract useful structural information from the three-dimensional maps. Key Words: Cryo-EM; cryoelectron microscopy; icosahedral virus; 3D reconstruction; subnanometer resolution; secondary structure elements; structural fitting 1.
Computational Inversion of Electron Tomography Images Using L2-Gradient Flows ∗
"... In this paper, we present a stable, reliable and robust method for reconstructing a three dimensional density function from a set of two dimensional electric tomographic images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L2-gradient flow is derived ..."
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In this paper, we present a stable, reliable and robust method for reconstructing a three dimensional density function from a set of two dimensional electric tomographic images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L2-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in temporal direction. The experimental results show that the proposed method is efficient and effective.
Comparison of single-particle analysis and electron tomography approaches: an overview
, 2008
"... Three-dimensional structure of a wide range of biological specimens can be computed from images collected by transmission electron microscopy. This information integrated with structural data obtained with other techniques (e.g., X-ray crystallography) helps structural biologists to understand the ..."
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Three-dimensional structure of a wide range of biological specimens can be computed from images collected by transmission electron microscopy. This information integrated with structural data obtained with other techniques (e.g., X-ray crystallography) helps structural biologists to understand the function of macromolecular complexes and organelles within cells. In this paper, we compare two threedimensional transmission electron microscopy techniques that are becoming more and more related (at the image acquisition level as well as the image processing one): electron tomography and single-particle analysis. The first one is currently used to elucidate the three-dimensional structure of cellular components or smaller entire cells, whereas the second one has been traditionally applied to structural studies of macromolecules and macromolecular complexes. Also, we discuss possibilities for their integration with other structural biology techniques for an integrative study of living matter from proteins to whole cells.
Contents lists available at ScienceDirect Journal of Structural Biology
"... journal homepage: www.elsevier.com/locate/yjsbi Automatic particle selection from electron micrographs using machine ..."
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journal homepage: www.elsevier.com/locate/yjsbi Automatic particle selection from electron micrographs using machine
Contents lists available at ScienceDirect Journal of Structural Biology
"... journal homepage: www.elsevier.com/locate/yjsbi Exploiting desktop supercomputing for three-dimensional electron microscopy ..."
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journal homepage: www.elsevier.com/locate/yjsbi Exploiting desktop supercomputing for three-dimensional electron microscopy
